Archive for coronavirus epidemics
ideal COVID¹⁹ chart
Posted in Statistics with tags bad graph, coronavirus epidemics, COVID-19, xkcd on April 16, 2020 by xi'an
ABC webinar, first!
Posted in Books, pictures, Statistics, University life with tags ABC, adaptive importance sampling, Approximate Bayesian computation, Bayesian neural networks, Bayesian nonparametrics, confinement, coronavirus epidemics, COVID-19, Kullback-Leibler divergence, normalising flow, webinar on April 13, 2020 by xi'an
The première of the ABC World Seminar last Thursday was most successful! It took place at the scheduled time, with no technical interruption and allowed 130⁺ participants from most of the World [sorry, West Coast friends!] to listen to the first speaker, Dennis Prangle, presenting normalising flows and distilled importance sampling. And to answer questions. As I had already commented on the earlier version of his paper, I will not reproduce them here. In short, I remain uncertain, albeit not skeptical, about the notions of normalising flows and variational encoders for estimating densities, when perceived as a non-parametric estimator due to the large number of parameters it involves and wonder at the availability of convergence rates. Incidentally, I had forgotten at the remarkable link between KL distance & importance sampling variability. Adding to the to-read list Müller et al. (2018) on neural importance sampling.
Monsieur le Président [reposted]
Posted in Books, Statistics, University life with tags Alexander Grothendieck, École Polytechnique, coronavirus epidemics, Emmanuel Macron, epidemiology, France, Jean-Michel Marin, severe testing, Société française de Statistique, survey sampling, tribune, Université de Montpellier on April 11, 2020 by xi'anLet us carry out screening campaigns on representative samples of population!
Mr President of the Republic, as you rightly indicated, we are at war and everything must be done to combat the spread of CODIV-19. You had the wisdom to surround yourself with a Scientific Council and an Analysis, Research and Expertise Committee, both competent, and, as you know, applied mathematicians, statisticians have a role to play in this battle. Yes, to predict the evolution of the epidemic, mathematical models are used at different scales. This allows us estimate the number of people infected in the coming weeks and months. We are at war and these predictions are essential to the development of the best control strategy. They inform political decisions. This is especially with the help of these items of information that the confinement of the French population has been decided and renewed.
Mr President we are at war and these predictions must be the most robust possible. The more precise they are, the better the decisions they will guide. Mathematical models include a number of unknown parameters whose values should be set based on expert advice or data. These include the transmission rate, incubation time, contagion time, and, of course, to initialize dynamic mathematical models, the number of covered individuals. To enjoy more reliable predictions, it is necessary to better estimate such crucial quantities. The proportion of healthy carriers appears to be a particularly critical parameter.
Mr President, we are at war and we must assess the proportions of healthy carriers by geographic areas. We do not currently have the means to implement massive screenings, but we can carry out surveys. This means, for a well-defined geographic area, to run biological tests on samples of individuals that are drawn at random and are representative of the total population of the area. Such data would come to supplement those already available and would considerably reduce the uncertainty in model predictions.
Mr. President, we are at war, let us give ourselves the means to fight effectively against this scourge. Thanks to a significant effort, the number of individuals that can be tested daily increases significantly, let’s devote some of these available tests to samples representative. For each individual drawn at random, we will perform a nasal swab, a blood test, let us collect clinical data and other items of information on its follow-up barriers. This would provide important information on the percentage of immunized French people. This data would open the possibility to feed mathematical models wisely, and hence to make informed decisions about the different strategies of deconfinement.
Mr. President, we are at war. This strategy, which could at first be deployed only in the most affected sectors, is, we believe, essential. It is doable: designing the survey and determining a representative sample is not an issue, going to the homes of the people in the sample, towards taking samples and having them fill out a questionnaire is also perfectly achievable if we give ourselves the means to do so. You only have to decide that a few of the available PCR tests and serological tests will be devoted to these statistical studies. In Paris and in the Grand Est, for instance, a mere few thousand tests on a representative population of individuals properly selected could better assess the situation and help in taking informed decisions.
Mr. President, a proposal to this effect has been presented to the Scientific Council and to the Analysis, Research and Expertise Committee that you have set up by a group of mathematicians at École Polytechnique with Professor Josselin Garnier at their head. You will realise by reading this tribune that the statistician that I am does support very strongly. I am in no way disputing the competence of the councils which support you but you have to act quickly and, I repeat, only dedicate a few thousand tests to statistics studies. Emergency is everywhere, assistance to the patients, to people in intensive care, must of course be the priority, but let us attempt to anticipate as well . We do not have the means to massively test the entire population, let us run polls.
Jean-Michel Marin
Professeur à l’Université de Montpellier
Président de la Société Française de Statistique
Directeur de l’Institut Montpelliérain Alexander Grothendieck
Vice-Doyen de la Faculté des Sciences de Montpellier
resignation of ERC president
Posted in University life with tags Academia Europaea, coronavirus epidemics, COVID-19, ERC, Europe, European Commission, European Research Council, European Union on April 10, 2020 by xi'an
[Reposting the ERC Scientific Council statement about the resignation of Mauro Ferrari:]
The ERC’s Scientific Council notes with regret the statement made by Mauro Ferrari concerning his resignation on 7 April. We here present the facts of the situation.
On Friday 27 March, all 19 active members of the ERC’s Scientific Council individually and unanimously requested that Mauro Ferrari resign from his position as ERC’s President.
This request was made for four reasons:
- During his three-month term in office, Professor Ferrari displayed a complete lack of appreciation for the raison-d’être of the ERC to support excellent frontier science, designed and implemented by the best researchers in Europe. Although voicing his support for this in public pronouncements, the proposals he made to the Scientific Council did not reflect this position. He did not understand the context of the ERC within the EU’s Research and Innovation Programme Horizon 2020.
- Since his appointment, Professor Ferrari displayed a lack of engagement with the ERC, failing to participate in many important meetings, spending extensive time in the USA and failing to defend the ERC’s programme and mission when representing the ERC.
- In contrast, Professor Ferrari made several personal initiatives within the Commission, without consulting or tapping into the collective knowledge of the Scientific Council, and instead using his position to promote his own ideas.
- Lastly, Professor Ferrari was involved in multiple external enterprises, some academic and some commercial, which took a lot of his time and effort and appeared on several occasions to take precedence over his commitment to ERC. The workload associated with these activities proved to be incompatible with the mandate of President of the Scientific Council.
Professor Ferrari subsequently resigned on 7 April 2020. Therefore, his resignation in fact followed a written unanimous vote of no confidence. In contrast, Professor Ferrari has stated that the reason for his resignation is that the Scientific Council did not support his call for the ERC to fund a special initiative focused on the COVID-19 virus. To address this point specifically, we did not support a special initiative because that is not our remit and the Commission’s Research and Innovation Directorate General, with which we are connected, was already very active in developing new programmes to support this research through the appropriate channels.
Indeed, many ERC funded researchers have been active for some time in researching the coronavirus family and many other equally dangerous pathogens. Over 50 ongoing or completed ERC projects supported for a total value of about EUR 100 million are contributing to the response to the COVID-19 pandemic by providing insights from several different scientific fields such as: virology, epidemiology, immunology, paths for new diagnostics and treatments, public health, medical devices, artificial intelligence, social behaviour, crisis management.
In addition, as stated on its website in reaction to the COVID-19 crisis, the ERC offers ‘grantees the flexibility to adjust their research project”. This is an efficient measure because several ERC grantees already enquired about the possibility of addressing COVID-19 related research in their ongoing ERC project. All this information is publicly available on the ERC website, which also includes testimonies from funded ERC grantees on how bottom-up frontier research is critical to deliver new – and sometimes unexpected – insights relevant for better understanding and fighting the COVID-19 pandemic, as well as for providing social behaviour and crisis management related solutions.
However, the ERC does not make calls for specific topics, since a guiding principle of ERC is that our researchers are free to pursue the goals they define and to decide on what they wish to work. In our view, this is a crucial way to generate the best science.
The Scientific Council wishes to clarify, in case of any doubt, that they absolutely endorse the view that scientific research will provide the best solutions to tackling pandemics, such as COVID-19.
Therefore, we regret Professor Ferrari’s statement, which at best is economical with the truth. This Scientific Council remains dedicated to pursuing the mission for which the ERC was established: the support of bottom-up ground-breaking research. It is also worth noting that despite the pandemic, the ERC Executive Agency is struggling against the odds to actively process applications for our Consolidator Grants and Starting Grants, which will support researchers throughout Europe to make the discoveries of the future.
Dorfman’s group testing
Posted in Books, Kids, Statistics, Travel with tags coronavirus epidemics, COVID-19, CREST, deconfinement, Robert Dorfman, syphilis, US Army, William Feller, WWII on April 9, 2020 by xi'an
A recent note by CREST researchers insists on using group testing to compensate for the shortage of test packages and testing personal, as done in several countries, towards deconfining individuals who are not infected. Or who are exhibiting the right antibodies. Reminding me of my first entry to the notion, in Feller’s book, of the method implemented by Robert Dorfman to test for syphilis prior to enlisting potential WW II soldiers. I would deem the idea useful for surveys, in identifying the proportion of infected or immunised persons, maybe less for giving the green light to leave one’s house as the logistics of merging the tests while keeping track of every individual could prove impossible.
